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X-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A mutations and DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 8% (w/v) PEG 4000, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.9 35.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.798 α = 90 b = 61.437 β = 106.447 c = 39.976 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 38.17 99.9 0.025 0.034 0.999 15.7 3.4 24423 23.1623401697
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.252 0.338 0.921 2.2 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2HDD 1.6 38.17 1.40888796396 24342 1204 99.6805896806 0.190614050402 0.18834877636 0.1906 0.235863688164 0.2372 26.5017300563
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.9104934855 f_angle_d 1.00456025375 f_chiral_restr 0.0473394368983 f_bond_d 0.00708185555911 f_plane_restr 0.00633961639965
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 913 Nucleic Acid Atoms 486 Solvent Atoms 207 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing